Results 41 to 50 of about 1,276,854 (326)
Optimization of sequence alignment for simple sequence repeat regions
BMC Research Notes, 2011 Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome.
Ogbonnaya Francis C +2 more
doaj +1 more source
The effect of sequence quality on sequence alignment [PDF]
Bioinformatics, 2008 Abstract Motivation: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, but are primarily used only for trimming sequences and generally ignored in subsequent analyses.
openaire +2 more sources
2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles [PDF]
, 2011 Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-
Hoi Shan Kwan +3 more
core +2 more sources
Local Alignment of DNA Sequence Based on Deep Reinforcement Learning
IEEE Open Journal of Engineering in Medicine and Biology, 2021 Goal: Over the decades, there have been improvements in the sequence alignment algorithm, with significant advances in various aspects such as complexity and accuracy. However, human-defined algorithms have an explicit limitation in view of developmental
Yong-Joon Song, Dong-Ho Cho
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Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing [PDF]
, 2003 Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological
Gilbert, D, Westhead, DR, Williams, A
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Aligning Multiple Sequences with Genetic Algorithm [PDF]
, 2009 The alignment of biological sequences is a crucial tool in molecular biology and genome analysis. It helps to build a phylogenetic tree of related DNA sequences and also to predict the function and structure of unknown protein sequences by aligning ...
Adebiyi, E. F. +2 more
core +1 more source
Lower bounds on multiple sequence alignment using exact 3-way alignment
BMC Bioinformatics, 2007 Background Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently
Colbourn Charles J, Kumar Sudhir
doaj +1 more source
Pairwise alignment incorporating dipeptide covariation
, 2005 Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated.
Altschul +34 more
core +1 more source
, 2020 Biological network alignment (NA) aims to find a node mapping between species' molecular networks that uncovers similar network regions, thus allowing for transfer of functional knowledge between the aligned nodes.
Gu, Shawn, Milenkovic, Tijana
core +1 more source
Fair Evaluation of Global Network Aligners [PDF]
, 2014 Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different ...
Crawford, Joseph +2 more
core +2 more sources